Gut feeling: His dream revealed bacteria’s secret power

As I enter his house in a leafy north Copenhagen suburb, Professor Oluf Borbye Pedersen tells me: »Keep your shoes on. This is how we do it here.«

Contrary to Danish custom, the professor invites the journalist to walk into the living room with his shoes on. We are to conduct an interview about his research into the gut microbiome — the ecosystem of billions of bacteria, viruses, and fungi in our intestines.

The idea is that when we keep our shoes on indoors, we bring new microorganisms into the home. This is good for our health, according to the head of research and chief physician. He has worked on the human genome and has been a microbiome scientist for the past 17 years.

He knows how important it is that we take care of our gut microbiome — like by ensuring that our homes contain a rich variety of microorganisms. Some of them will, sooner or later, find their way into our intestines and be of benefit.

Hormone-like compound

For the past six years, Oluf Borbye Pedersen has led a project that aims to unravel more of the microbiome mysteries. He and his research team have discovered the first known molecules with distinct biological effects on the body.

We can change animals’ pain thresholds simply by altering their gut microbiome

Oluf Borbye Pedersen

The breakthrough involves two signalling proteins made by certain strains of bacteria in the gut. According to Oluf Borbye Pedersen, the signalling proteins resemble the hormone irisin in molecular structure — a hormone that we produce in our muscles when we exercise.

The signalling proteins have proven to have some of the same, wide, beneficial effects as irisin — which is often referred to as a sport hormone.

»That’s why there’s so much attention around this discovery, and that’s why the University of Copenhagen patented it already two years ago,« says Oluf Borbye Pedersen.

Humans are not the pinnacle of evolution

Oluf Borbye Pedersen played a role in a landmark scientific discovery 15 years ago that also involved the life of gut microorganisms. The discovery shaped both his perspective as a health expert and his perspective on humans and their place in nature:

»The importance of the microbiome was hidden from us until we acquired the genetic technologies and supercomputer capacities to reveal it,« he says.

Until 15 years ago, nobody really knew what was going on with the gut’s microorganisms. Oluf Borbye Pedersen helped shed a light on it — and he encourages us to make friends with our microbiome if we want to live well.

He also believes we should stop seeing humans as the pinnacle of evolution.

»Instead, we should understand ourselves as being like temporary guests on a planet ruled by bacteria. It belongs to them — we live in a collective with them — and we are no more important than they are,« says Oluf Borbye Pedersen.

The big breakthrough

Fifteen years ago, he and a group of European and Chinese researchers were the first in the world to use DNA technology and supercomputers to reveal what our gut microbiome consists of, and how it functions.

They found 3.3 million genes in the microbiome of the human digestive tract. By way of comparison, the human genome — which determines how the cells in our body are constructed — consists of only about 23,000 genes.

Their breakthrough made it to the cover of the prestigious science journal Nature in June 2010, accompanied by an article titled The Tale of Our Other Genome.

No one would believe them

Oluf Borbye Pedersen has been a researcher for 53 years, but his most recent major project — which ran from 2019 to 2025 — was the hardest to complete.

Even after they had discovered the two signalling compounds, it took his research group two years to get a leading international science journal to accept and publish an article on their findings:

»There was a lot of resistance because no one wanted to believe that bacteria have the genomic capacity to produce hormones. The breakthrough seemed to be too revolutionary, and it may have been seen as too provocative for the four peer reviewers who read our article and repeatedly asked for more experimental evidence. It took a lot of perseverance to keep the research team motivated,« says Oluf Borbye Pedersen.

Maybe in pill form

It had already been proven that by changing the gut microbiome in lab animals, it was possible to alter their behaviour, according to Oluf Borbye Pedersen.

»We and other researchers can create curious animals with strong cognitive functions. We can create anxious animals, and we can change animals’ pain thresholds simply by changing their gut microbiome,« he says.

This is partly explained by the fact that the gut produces at least seven different neurotransmitters — like serotonin and dopamine — that regulate brain function from the intestines.

But the project Oluf Borbye Pedersen and his international team have worked on for the past six years is the first to show that the gut microbiome also contributes to the body’s hormonal balance — and this has made waves in academic research circles.

Oluf Borbye Pedersen hopes the new discoveries can be used to develop a new type of pharmabiotic that helps people lose weight. But even if basic research can be turned into medicine, it will take 10–15 years and a huge financial investment.

»It’s also possible that the bacteria in our microbiome that produce the irisin-like molecules — called RORDEP1 and RORDEP2 — could be developed into a dietary supplement, a so-called second-generation probiotic. They might prevent chronic diseases such as diabetes, obesity, and osteoporosis, and they might also be developed to treat a range of chronic illnesses,« he says.

From intuition to research

The beginning of the latest research project was not easy — and perhaps a little unusual.

»It all started with what I would call an intuitive dream in 2017. I dreamt about the many genes in the gut microbiome and that they were capable of producing hormones resembling insulin and others. In the dream, it was very, very clear to me,« he says.

He ruminated on this dream for a good six months before finally acting on it.

It was really hard to maintain our enthusiasm, joy, intellect, and intuition

Oluf Borbye Pedersen

»At first, I kept the thoughts to myself. I eventually shared them with some of my Danish postdocs and senior researchers,« says Oluf Borbye Pedersen.

Initially, things didn’t go quite as he had hoped.

»I think I asked four of my talented postdocs whether they wanted to do research based on this idea, but they all thought it was too wild. They felt the risk of failure was too high,« he says.

But a positive reply came from a researcher on the opposite side of the globe.

»At one point I met an exceptionally talented researcher, Yong Fan, who had completed his PhD at an elite university in China. He could work with bioinformatics, computer science, and more. I managed to convince him of the possible relevance of my dream,« says Oluf Borbye Pedersen.

He asked Yong Fan right away to start searching for genes in the gut microbiome whose molecular structure resembled hormones already produced by the human body. Yong Fan’s specialised knowledge was crucial for this.

Months went by with no results, but in the third week of January 2019, Oluf Borbye Pedersen and his research group  got a hit: The hormone irisin.

They had now shown that gut bacteria could produce a compound similar to one of the hormones that already function in the human body. But despite the major breakthrough, the years that followed were extremely demanding.

»There were many dead ends in our work, and we experienced many ups and downs. The pressure on us was intense, and it was really difficult to maintain our enthusiasm, joy, intellect, and intuition,« says Oluf Borbye Pedersen.

What do the bacteria want from us?

When the pressure became too much, Oluf Borbye Pedersen sought comfort in the words of Albert Einstein. The thoughts of the creator of the theory of general relativity helped him stay resilient.

»Intellectually, Einstein was an elitist, but he had the ability to withdraw and let his intuition and dreams take over. Einstein believed that intuition and our capacity to dream are the most important gifts humans have received, and he described the intellect as the servant of intuition. He was also deeply humble when it came to the great unanswered questions of science,« says Oluf Borbye Pedersen.

Einstein described the intellect as the servant of intuition

Oluf Borbye Pedersen

That humility is something to keep in mind, he says, when researching what he himself calls humanity’s astronomical microbiome.

»We live in symbiosis with bacteria, and we cannot thrive without them. The bacteria were here before us, and I call for humility — what do the astronomically numerous microorganisms actually want from us? That is the big, central question, bordering on the philosophical,« says Oluf Borbye Pedersen.

The bacteria and their accompanying microbes, he believes, are in control when it comes to our health. Nowadays there are, in his view, three key functional areas that doctors know a great deal about.

»The first is metabolism — the body’s way of converting food and drink into fuel and building blocks, while producing a range of substances that regulate our health. The second is immune competence. And the third is brain biology, which likely governs what we think, feel, and do,« says Oluf Borbye Pedersen.

He says that right now — 15 years after the revolutionary article in Nature — we are still barely scratching the surface in terms of understanding what the microbiome means for us. But he is convinced that we must take care of our microbiome if we want to live healthily.

»We humans may carry the genes for around 30 chronic diseases — like Parkinson’s, diabetes, and obesity. On their own, they cause no harm. It is only when they are exposed to an unhealthy lifestyle that they become a problem. And what affects the expression of our disease genes? An unhealthy gut microbiome. But if you keep your gut microbiome healthy — by eating mostly plant-based food, exercising daily, and avoiding smoking or drinking too much alcohol — then your microbiome will work for you and probably not activate your inherited disease genes,« concludes Oluf Borbye Pedersen.

This article was first written in Danish and published on 22 August 2025. It has been translated into English and post-edited by Mike Young.